Public metagenome datasets annotated using SingleM

These data underlie the community profiles shown at https://sandpiper.qut.edu.au

The community profiles are in “unfilled SingleM condensed” format. You may wish to convert them to use relative abundances, etc. using singlem summarise --output-taxonomic-profile-with-extras, which operates without loading the entire profile into memory (unlike some other conversions of the summarise command). For more details and information, see https://wwood.github.io/singlem/tools/summarise.

As well as this, metadata files are provided, which contain the following columns (all are one run per row in the TSV/CSV)

parsed_metadata:

1. run
2. latitude
3. longitude
4. depth
5. temperature
6. collection_year
7. collection_month

per_acc_summary:

1. sample (i.e. run)
2. root_coverage (total coverage of prokaryotes)
3. species_coverage (coverage assigned to the species level)
4. top1_order_fraction (fraction of coverage assigned to the most common order out of the total coverage assigned to order level)
5. top3_order_fraction (total fraction of coverage assigned to the 3 most common orders out of the total coverage assigned to order level)
6. low_complexity (yes/no/missing: yes if top1_order_fraction is > 95%, indicating that the sample may not be a true microbial community)
7. known_species_fraction (coverage assigned to the species level compared to root_coverage, as a %)
8. bacterial_archaeal_bases (estimated number of bases in reads that are prokaryotic, from SPF)
9. metagenome_size (bp)
10. singlem prokaryotic fraction (SPF)
11. average_bacterial_archaeal_genome_size (AGS of prokaryotes)
12. warning (whether singlem prokaryotic_fraction raised a warning)
13. prediction (euk-host-associated or not? An ML prediction)
14. host_or_not (annotated euk-host-association from the “organism” field if possible, or failing that, the ML prediction thereof)
15. organism (official metadata of biosample)

kingfisher_metadata:

A tab-separated file containing biosample-related metadata downloaded for each run, generated using kingfisher annotate. It has many columns, because every submitter can create new kinds of metadata.

Changelog

version 2.1.0

• Integration of GlobDB R232 community profiles.

version 2.0.1

• Fixed formatting and data in GTDB community profiles. All other data is unchanged (thanks to Cliff Bueno de Mesquita for spotting the issue),

version 2.0.0

• Additional public metagenomes analysed = 205,695, total metagenomes screened -> 913,165.
• Integ
  

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